Locus 7664

Sequence ID 2L_DroMel_CAF1
Location 21,356,329 – 21,356,459
Length 130
Max. P 0.999405
window12312 window12313 window12314

overview

Window 2

Location 21,356,329 – 21,356,419
Length 90
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 77.86
Mean single sequence MFE -20.05
Consensus MFE -14.70
Energy contribution -15.64
Covariance contribution 0.94
Combinations/Pair 1.20
Mean z-score -2.78
Structure conservation index 0.73
SVM decision value 3.32
SVM RNA-class probability 0.998990
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21356329 90 + 22407834
UC-U-U--UUUUUUCAUAAAUUAAAUUGUUGCAAGGGUAUAUAAGCUUCGGCUUGCCGAAGCUAGCUUCCUUUCUUGUUU---UUUUAUAACCUGUC
..-.-.--.......(((((..((((....(.(((((......((((((((....))))))))....))))).)..))))---.)))))........ ( -18.80)
>DroSec_CAF1 65761 79 + 1
----------------UAAAUUAAAUUUUUGCAAGGGUACAUAAGCUUCGGCUUGCCGAAGCUAGCUUCCUUCCUUGUUU--UUUUUAUAACCUGUC
----------------.....((((.....(((((((......((((((((....))))))))........)))))))..--..))))......... ( -21.74)
>DroEre_CAF1 48794 84 + 1
UUGG-UA--UUUUUCUUAAAUAAAAUCAU-----AAGUACAUAAGUUUCGGCUUGCCGAAGCUAGCUU----UGUUGAUUU-UUUUUAUAACCUGUC
..((-(.--.......((((.(((((((.-----((((.....((((((((....)))))))).))))----...))))))-).))))..))).... ( -18.80)
>DroYak_CAF1 52823 97 + 1
UUGGGUAUUUUUUUCUUAAAUUAAAUUAUUGCAAGGGUACAUAAGCUUCGGCUUGCCGAAGCUAGCUUCCUUUCUUGUUUUGUUUUUAUAACCUGUC
..((((((((.......))))((((.((..(((((((......((((((((....))))))))........)))))))..))..))))..))))... ( -20.84)
>consensus
UU_G_U___UUUUUCUUAAAUUAAAUUAUUGCAAGGGUACAUAAGCUUCGGCUUGCCGAAGCUAGCUUCCUUUCUUGUUU__UUUUUAUAACCUGUC
..............................(((((((......((((((((....))))))))........)))))))................... (-14.70 = -15.64 +   0.94)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,356,329 – 21,356,419
Length 90
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 77.86
Mean single sequence MFE -18.40
Consensus MFE -13.40
Energy contribution -14.78
Covariance contribution 1.38
Combinations/Pair 1.00
Mean z-score -2.92
Structure conservation index 0.73
SVM decision value 3.57
SVM RNA-class probability 0.999405
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21356329 90 - 22407834
GACAGGUUAUAAAA---AAACAAGAAAGGAAGCUAGCUUCGGCAAGCCGAAGCUUAUAUACCCUUGCAACAAUUUAAUUUAUGAAAAAA--A-A-GA
......(((((((.---........((((.....((((((((....)))))))).......))))............))))))).....--.-.-.. ( -17.90)
>DroSec_CAF1 65761 79 - 1
GACAGGUUAUAAAAA--AAACAAGGAAGGAAGCUAGCUUCGGCAAGCCGAAGCUUAUGUACCCUUGCAAAAAUUUAAUUUA----------------
...............--......(.((((..((.((((((((....))))))))...))..)))).)..............---------------- ( -21.30)
>DroEre_CAF1 48794 84 - 1
GACAGGUUAUAAAAA-AAAUCAACA----AAGCUAGCUUCGGCAAGCCGAAACUUAUGUACUU-----AUGAUUUUAUUUAAGAAAAA--UA-CCAA
....(((..((((.(-((((((...----..((.((.(((((....))))).))...))....-----.))))))).)))).......--.)-)).. ( -14.30)
>DroYak_CAF1 52823 97 - 1
GACAGGUUAUAAAAACAAAACAAGAAAGGAAGCUAGCUUCGGCAAGCCGAAGCUUAUGUACCCUUGCAAUAAUUUAAUUUAAGAAAAAAAUACCCAA
....((.(((.............(.((((..((.((((((((....))))))))...))..)))).)..(((......)))........))).)).. ( -20.10)
>consensus
GACAGGUUAUAAAAA__AAACAAGAAAGGAAGCUAGCUUCGGCAAGCCGAAGCUUAUGUACCCUUGCAAUAAUUUAAUUUAAGAAAAA___A_C_AA
.......................(.((((..((.((((((((....))))))))...))..)))).).............................. (-13.40 = -14.78 +   1.38)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,356,360 – 21,356,459
Length 99
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 92.27
Mean single sequence MFE -24.84
Consensus MFE -23.66
Energy contribution -23.09
Covariance contribution -0.56
Combinations/Pair 1.15
Mean z-score -2.05
Structure conservation index 0.95
SVM decision value 1.75
SVM RNA-class probability 0.975282
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 21356360 99 + 22407834
GGUAUAUAAGCUUCGGCUUGCCGAAGCUAGCUUCCUUUCUUGUUU---UUUUAUAACCUGUCGUUGGCAAAACUCUCCACAACGGCAAAACACUAAGAUGUU
(((.((((((((((((....))))))))(((..........))).---...)))))))((((((((.............))))))))............... ( -25.42)
>DroSec_CAF1 65780 100 + 1
GGUACAUAAGCUUCGGCUUGCCGAAGCUAGCUUCCUUCCUUGUUU--UUUUUAUAACCUGUCGUUGGCAAAACUCUCCACAACGGCAAAACACUAAGAUGUU
...((((.((((((((....))))))))......(((...(((((--...........((((((((.............)))))))))))))..))))))). ( -25.22)
>DroEre_CAF1 48821 97 + 1
AGUACAUAAGUUUCGGCUUGCCGAAGCUAGCUU----UGUUGAUUU-UUUUUAUAACCUGUCGUUGGCAAAACUCUCCACAACGGCAAAACACCAAGAUGUU
...((((.((((((((....)))))))).....----.........-...........((((((((.............))))))))..........)))). ( -22.42)
>DroYak_CAF1 52858 102 + 1
GGUACAUAAGCUUCGGCUUGCCGAAGCUAGCUUCCUUUCUUGUUUUGUUUUUAUAACCUGUCGUUGGCAAAACUCUCCAUAACGGCAAAACACCAAGAUGUU
((......((((((((....)))))))).....))..(((((...(((((........((((((((.............))))))))))))).))))).... ( -26.32)
>consensus
GGUACAUAAGCUUCGGCUUGCCGAAGCUAGCUUCCUUUCUUGUUU__UUUUUAUAACCUGUCGUUGGCAAAACUCUCCACAACGGCAAAACACCAAGAUGUU
...((((.((((((((....))))))))..............................((((((((.............))))))))..........)))). (-23.66 = -23.09 +  -0.56)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:42:16 2006